add fix for alignments correctly saving as XML in BEAUti #1150

src/beast/base/evolution/alignment/Alignment.java

@@ -279,6 +279,20 @@ public void initAndValidate() {
         Log.info.println(toString(false));
     }
 
+
+    /** hack to suppress empty TaxonSets in XML output
+     * this was no problem when Alignments was a CalculationNode,
+     * but became an issue changing it to a StateNode  
+     * TODO: fix this**/
+    @Override
+    public List<Input<?>> listInputs() {
+    	List<Input<?>> inputs = super.listInputs();
+        if (taxonSetInput.get() != null && taxonSetInput.get().getTaxonCount() == 0) {
+        	inputs.remove(taxonSetInput);
+        }
+        return inputs;
+    }
+
     /**
      * Initializes data types using
      * {@link PackageManager#find(Class, String[]) PackageManager.find}